forqs

forqs is a forward-in-time population genetics simulation that tracks
individual haplotype chunks as they recombine each generation. forqs also
also models quantitative traits and selection on those traits.

forqs is implemented as a command-line C++ program, using a modular design
that gives the user great flexibility in creating custom simulations. It is
freely available with a permissive BSD license. You can obtain the latest
binary package (Linux, OSX, Windows) from the downloads
page.